American Gut: an Open Platform for Citizen Science Microbiome Research

By Daniel McDonald, Embriette R. Hyde, Justine W. Debelius, James T. Morton, Antonio Gonzalez, Gail L Ackermann, A. Aksenov, Bahar Behsaz, C. Brennan, Yingfeng Chen and 48 more. mSystems, 2018

775 citations recorded by the source corpus.

We show that a citizen science, self-selected cohort shipping samples through the mail at room temperature recaptures many known microbiome results from clinically collected cohorts and reveals new ones. Of particular interest is integrating n = 1 study data with the population data, showing that the extent of microbiome change after events such as surgery can exceed differences between distinct environmental biomes, and the effect of diverse plants in the diet, which we confirm with untargeted metabolomics on hundreds of samples. ABSTRACT Although much work has linked the human microbiome to specific phenotypes and lifestyle variables, data from different projects have been challenging to integrate and the extent of microbial and molecular diversity in human stool remains unknown. Using standardized protocols from the Earth Microbiome Project and sample contributions from over 10,000 citizen-scientists, together with an open research network, we compare human microbiome specimens primarily from the United States, United Kingdom, and Australia to one another and to environmental samples. Our results show an unexpected range of beta-diversity in human stool microbiomes compared to environmental samples; demonstrate the utility of procedures for removing the effects of overgrowth during room-temperature shipping for revealing phenotype correlations; uncover new molecules and kinds of molecular communities in the human stool metabolome; and examine emergent associations among the microbiome, metabolome, and the diversity of plants that are consumed (rather than relying on reductive categorical variables such as veganism, which have little or no explanatory power). We also demonstrate the utility of the living data resource and cross-cohort comparison to confirm existing associations between the microbiome and psychiatric illness and to reveal the extent of microbiome change within one individual during surgery, providing a paradigm for open microbiome research and education. IMPORTANCE We show that a citizen science, self-selected cohort shipping samples through the mail at room temperature recaptures many known microbiome results from clinically collected cohorts and reveals new ones. Of particular interest is integrating n = 1 study data with the population data, showing that the extent of microbiome change after events such as surgery can exceed differences between distinct environmental biomes, and the effect of diverse plants in the diet, which we confirm with untargeted metabolomics on hundreds of samples.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/cb349a7647eaa37f5806b435e0f8e2918980a9a2

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Citations in the corpus

Effect of Diet on the Gut Microbiota: Rethinking Intervention Duration (2019, background): “Dietary diver ity has been associated with microbial diversity [78].”
LinDA: linear models for differential abundance analysis of microbiome compositional data (2021, methodology): “We also tested on a massive dataset of the similar scale of the AmericanGut project [42] (m = 5000 and n = 10000).”
Greengenes2 unifies microbial data in a single reference tree (2023, neutral): “In two large human stool cohorts 14,16 where both 16S and shotgun data were generated on the same samples, we find that Bray–Curtis 17 (non-phylogenetic) ordination fails to reconcile at the feature level (Fig.”
Multimodal biomedical AI (2022, methodology): “As another example, the American Gut Project collects microbiome data from self-selected participants across several countries 94 .”
High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing (2021, methodology): “Here, we applied the PacBio UMI method to generate 253,089 high-quality, full-length bacterial rRNA operon sequences from 70 human fecal samples collected by the American Gut Project 22 .”